Dr. Weir awakens in a locked room at Willoughby State Psychiatric Hospital near Washington, D.C. When she demands to know how she arrived there from the Pegasus galaxy, she's horrified to hear that she has never really left Earth. Her psychiatrist, Dr. Adam Fletcher, slowly and gently reveals that a car crash killed her boyfriend Simon three weeks ago. Then, a mere three days ago, her mind broke down under stress and sorrow while she was negotiating a high-pressure U.N. treaty. She suffered a brief reactive psychosis - a temporary break from reality that left her in a near catatonic state, wracked with vivid hallucinations, for several days. Her memories of the past two years are false.
At first, Weir refuses to believe that her time in Atlantis was a dream, but when Gen. Jack O'Neill visits her, he insists that he's never even heard of a stargate. Instead, he claims that he met her during the treaty negotiations. Weir's mother reassures her that Fletcher and O'Neill are telling the truth, and Weir's confidence in her own sanity is weakened even further by strange visions and odd noises that stalk her during these conversations and haunt her hospital room at night.
Eventually, in desperation and confusion, Weir consents to take the powerful medications that Dr. Fletcher has prescribed. She improves, and soon Fletcher allows her to return to her cozy house and her beloved dog. A teaching job awaits her at Georgetown University, and O'Neill urges her to return to the negotiation table, as well.
Just when her life seems back on track, however, Weir begins suffering more terrifying hallucinations. Despite Fletcher's best reassurances, she again becomes convinced that there's more happening to her than a mental breakdown. She feels as though some unknown being is struggling to send an urgent message to her - a message from the world of her hallucination.
In fact, Sheppard is sending the message - from Atlantis. Weir is in a coma there after an attack by Asuran nanites, which have flooded her body and want to take over her mind. Sheppard is by her side, speaking to her and urging her to fight, while Beckett, with McKay's help, risks a dangerous last-resort treatment. It fails. In the end, only Weir can win the battle for her own mind.